We often talk as if "sympathy" were the sure symptom of a reader's satisfaction, the evidence of a character - usually the "hero" or "heroine" - brought successfully to life. Kate Grenville's The Secret River initially seems as if it were indeed keen to elicit sympathy for its protagonist. Yet she sets out to win the reader's allegiance for an unusual purpose. She structures her narrative so as to obtain sympathy for a character who, we eventually realise, is going to do something unforgiveable.

A short prologue headed "Strangers" warns us of a conflict to come. William Thornhill, transported as a convict to Australia in 1806, is passing his first night in the penal colony of New South Wales. Unable to sleep, he leaves his hut and suddenly finds himself confronted by a man "as black as the air itself", holding a spear. He shouts at him, as if he were a stray dog. Silently the man disappears into the surrounding forest. It is a cameo of fear and aggression. It foreshadows a future confrontation.

After this opening, part one of The Secret River takes us back in time to London at the end of the 18th century to see the young Thornhill, born into near-destitution, struggling to survive. We already know, of course, where he is destined to end up. The account of the first 30 years of Thornhill's life, of the poverty of his family and his struggles to make good, seems designed to win our sympathy. Through no fault of his own, he loses his promising future as a Thames waterman, takes to petty theft and only narrowly escapes the gallows. Instead he is sentenced to transportation, though his wife, Sal, and their children are allowed to travel with him.

Sympathy is not just the consequence of a hard-luck story; it is the product of a narrative method. Though narrated in the third person, this story is told entirely from Thornhill's point of view. The narrator has unimpeded access to his thoughts: "He knew . . . he saw . . . he remembered". Much of the narrative is in free indirect style, adopting the habits of thought and speech of the character himself. Even when not directly reporting Thornhill's thoughts, it uses his idioms. It is this intimacy with the novel's protagonist that will become discomfiting, as we come to share what he keeps secret from his wife.

He thinks that he is protecting her from horrors. Soon after his arrival he encounters another "emancipee", Smasher, who proudly brandishes the severed hands of an Aboriginal whom he has caught stealing from him. As Thornhill rows away he looks back through a telescope and sees what he at first thinks is "a beast hung up for butchering", but then understands is "the body of a black man", hanging from a tree, horribly mutilated. He tells his wife nothing about this. Later he finds out that Smasher and a fellow settler have captured an Aboriginal woman whom they keep chained and rape at their pleasure. He sees the woman, and therefore we are made to see her too, but he will tell no one. Imagining telling his wife, "even thinking the words in his own mind - filled him with shame". The narrative's word for what he has seen is also his word. "He had done nothing to help her. Now the evil was part of him." This, too, is free indirect style, the character's verdict on himself.

Fiction often attempts to draw the reader into the mind of a character who acts badly. It is unusual, however, for a novel to work hard to win your sympathy for a central character, only to destroy that sympathy. Now you see the point of the novelist's peculiar decision on what to call him. Thornhill's wife is "Sal", the two useless yet potentially murderous ex-convicts he takes on as servants are always called "Ned" and "Dan", yet the novel always calls Thornhill by his surname, never friendly enough to use his first name.

The very blurb on the novel's cover warns us that Thornhill will finally have to make a terrible "decision". This reflects the sense of foreboding that the novel engineers. From the prologue onwards, the threat of violence hangs over it, implicit in the white settlers' obsession with the mysterious "blacks". "They all going to be real sorry," says the repellent Smasher, after he has been punched by Blackwood, an ex-convict who secretly lives with an Aboriginal woman and has had a child by her. Sal predicts "trouble", and the reader predicts it too. The sense of some impending catastrophe is almost painful; you know that it will be seen through Thornhill's eyes, and you suspect that this will require his involvement.

Thornhill makes his decision. In its aftermath, like some plebeian Macbeth, he just washes his hands vigorously, "over and over against each other, slippery with soap", while his wife chooses not to ask any questions that might challenge him to a lie. "He had his answers ready." But he does not need them. She lets the choices into which the novel has led him remain untalked of. What has happened becomes "a little shadow; the thing not spoken of". But the marriage accommodates such silence. He betrays our sympathy and, as experienced novel readers, we might expect him to be punished, but even this solace is to be denied us.

• John Mullan is professor of English at University College London. Join him and Kate Grenville for a discussion on 4 February at 6.30pm. The talk will begin at 7pm, at the Scott Room, The Guardian, Kings Place, 90 York Way, London N1 9GU. Tickets £8 (includes a glass of wine). Email book.club@theguardian.com or phone 020 3353 2881.